bioinformatics-seq-qc-pipelinelisted

# Quality-control sequencing data before analysis > Read-level QC, adapter trimming, contamination screens, and reproducible QC reporting. **Track:** 🧬 Biotech & Pharma · **Domain:** Bioinformatics · **Level:** intermediate · **~45 min** **Who this is for:** Bioinformaticians, Lab Scientists, Regulatory Affairs, Genetic Engineers, Clinical Data Managers ## When to Use This Skill Read-level QC, adapter trimming, contamination screens, and reproducible QC reporting. Use it whenever a matching task appears in conversation — the agent loads these instructions on demand. ## Steps 1. Run read-level QC: per-base quality, GC bias, duplication profiles 2. Trim adapters/low-quality tails with documented parameter versions 3. Screen contamination against expected organism panels 4. Verify reference genome build matches annotation versions exactly 5. Emit multi-sample QC summary tables for batch comparison 6. Pin tool versions in a workflow manager (Snakemake/Nextflow) for reruns ## Common Pitfalls - Mixed genome builds between alignment and annotation - Batch effects mistaken for biological signal ## Commands **Install with skills CLI** ```bash npx skills add aniruddhaadak80/skills --skill bioinformatics-seq-qc-pipeline ``` **Install globally** ```bash npx skills add aniruddhaadak80/skills --skill bioinformatics-seq-qc-pipeline -g ``` --- Part of [aniruddhaadak80/skills](https://github.com/aniruddhaadak80/skills) · Browse all at https://skills.sh/aniruddhaadak80/skills